|
| Status |
Public on Jan 25, 2023 |
| Title |
crb2a m289/m289 retina rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Danio rerio |
| Characteristics |
tissue: retina
hpf: 56
genotype: crb2a (m289/m289)
|
| Growth protocol |
zebrafish were harvested at appropriate time points (hpf), retinal regions dissected
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High quality genomic DNA was isolated using standard protocols.
RRBS libraries were constructed using the Ovation® RRBS Methyl-Seq (Nugen) kit using standard protocols
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Basecalls were processed to FASTQ reads using NuGENs custom python scripts for RRBS analysis that can be found at [NuGEN company provided pipeline](https://github.com/nugentechnologies/NuMetRRBS).
Reads were trimmed using Trimgalore further processed using NuGEN Diversity Triming
Reads were aligned using Bismark (v0.22.3) using the parameter --bowtie2
Resulting BAM files were sorted by coodinates and duplicates were processed with NuDUP from NuGEN
Methylation was assessed using Methykit (Bioconductor)
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include CpG tables from Methylkit analysis (processBismarkAln).
|
| |
|
| Submission date |
Jun 24, 2021 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Mariya Moosajee |
| Organization name |
UCL
|
| Department |
Institute of Ophthalmology
|
| Street address |
11-43 Bath Street
|
| City |
London |
| ZIP/Postal code |
EC1V 9EL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE178842 |
Reduced representation bisulfite sequencing (RRBS) of the retina of crumbs 2a (crb2a m289/m289) zebrafish model of Leber congenital amaurosis and retinitis pigmentosa. |
|
| Relations |
| SRA |
SRX11220402 |
| BioSample |
SAMN20002877 |
